There is provided a method of calculating physical properties of a periodic structure. At least one physical property related to reflectivity or transmittance of a periodic structure is measured, and then, at least one physical property related to reflectivity or transmittance of a virtual periodic structure is calculated to obtain corresponding physical properties from the virtual periodic structure. The at least one calculated physical property is compared with the at least one measured physical property. When the virtual periodic structure is horizontally divided into a plurality of layers, at least three substances can have horizontally repeated periods in the middle layers of the divided structure. In accordance with an embodiment of the present invention, the microscopic formation of the periodic structure including a native oxide layer formed on the periodic structure or an intentionally formed surface coating layer thereon can be nondestructively and accurately tested.